P212121

Alexander McPherson will be a familiar name to those who read this blog. The Futures in Biotech interviews Alexander discusses a brief history and covers many of the basics of X-ray crystallography. The interview segues into various aspects of synchrotrons then to crystallization of Teslas and Toyota Corollas. A nice tip of the hat to all the programmers that have really help crystallography progress.

Is biochemistry the lagging field in protein crystallography? Is there an example of protein that doesn’t crystallization because it is too pure?

Here are two excellent movies that show the protein crystallization of lysozyme.

The first movie from Bernard Rupp does an excellent job of showing nucleation.

The second movie from George Sheldrick is a does a great job of showing the actual crystal growth.

Enjoy.

Donald Sadoway from MIT gives a concise introductory lecture on the diffraction of crystals, enjoy!

7:15 Begins deriving Bragg’s Law
8:10 Expresses the joys of teaching around cell phones.
13:03 Body Center Cubic case relating to Bragg’s Law
16:08 Starts discussing why systematic absences appear
21:10 Indexing a Crystal Structure based on Powder Diffraction
27:00 The Thrill of Discovery
36:20 Laue Diffraction
40:15 Rotational Symmetry: ‘fold’
46:35 NIST Story and 5 fold symmetry (good stuff)

There is a line between sweeping generalizations and explaining every minute detail.

Generalizations are where you learn and details are where you earn (Muhammad Ali, eat your heart out).

Often labs have a generalized working protocol for their experiments. Lab procedures provide a foundation for learning especially concerning instrumentation and often have to be adjusted depending on the results. These necessary adjustments provide the opportunity for insight and this is where the minute details become important.

The middle ground is following a published procedure. A published procedure often gives the illusion of an easy step by step path to follow. The expectation is that by following the protocol from a paper that you will be able to achieve the same results. Since science is based on the reproducibility of experimental results this seems like a reasonable assumption. In actuality, papers are often incomplete in their material and methods sections. For example, researchers themselves can difficulty reproducing even their lab members own results.

In one such case, only one person could attain crystals of a particular protein and despite numerous attempts by fellow lab members they could achieve the same result. They decided to follow along the one person that was able to attain the crystals in order to see what they were doing differently. It ended up that the successful researcher was a devout coffee lover and had quite shaky hands when setting up crystal trays. The shaky hands resulted in better mixing between the condition and protein causing crystal formation.

Unfortunately, the critical piece of the puzzle (drinking 4 cups of coffee before setting up crystal trays) doesn’t make it into a paper’s material and methods section. The solution is to have reasonable expectations of descriptions in a methods section, but of course this is a sweeping generalization.

Following up on our previous discussion about the Protein Structure Initiative (PSI)

Nick points us to an excellent paper in Nature Methods (don’t forget the supplementary information) that provides insights gained through working with over 10,000 proteins. The paper covers the following topics:

1) Designing the cDNA constructs
2) Cloning method (Ligation-independent cloning)
3) Expression screening in 96-well format
4) Large-scale protein expression and purification
5) Protein characterization
6) Induction of chaperones
7) Co-expression

I really appreciated the easy to read tables. Check it out and let me know what you think.

The P212121 Store has been going really well! We have been able to team up with awesome manufactures and massively increase our inventory. The store launched with just 8 chemicals and now has over 100! We expect that number to double in the next couple of months. However, it’s not just about how many items we carry, but which items and that is where your feedback comes in.

P212121 – Client Feedback

The survey is really short so if there is something that you want to share on design, features, pricing, product descriptions, the search function, etc… please email us at: hereisanidea@p212121.com . Yes, technically you’re doing our work for us, but it’s mutually beneficial since we’ll do our best to provide what you need. Thanks!

We have discussed various databases on carbohydrates and small molecules, however we have yet to touch on lipids.

The LipidBank began in 1989 and now contains just over 7000 structures.

The database can be refined by name, source, chemical synthesis, biological activity or formula as well as by type (fatty acids, soluble vitamins and phospholipids). The lipids within the database contain structural, spectral and literature information. Although the database has not been updated to since 2007 it is certainly useful.